conda-forge / conda-forge/julia-feedstock
CHOLMOD Warning, Linking Issues on Mac
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Description
### Solution to issue cannot be found in the documentation.
- [X] I checked the documentation.
### Issue
Installing Julia just from conda-forge onto an Intel Mac results in CHOLMOD warning. I am not sure if what it states is true, as apparently this warning has been erroneous in the past:
```
» conda create --override-channels --channel conda-forge -n julia-test julia
…
» conda activate julia-test
» julia --project=.
_
_ _ _(_)_ | Documentation: https://docs.julialang.org
(_) | (_) (_) |
_ _ _| |_ __ _ | Type "?" for help, "]?" for Pkg help.
| | | | | | |/ _` | |
| | |_| | | | (_| | | Version 1.10.2 (2024-03-01)
_/ |\__'_|_|_|\__'_| | https://github.com/conda-forge/julia-feedstock
|__/ |
julia> using SparseArrays
┌ Warning: CHOLMOD version incompatibility
│
│ Julia was compiled with CHOLMOD version 4.0.4. It is
│ currently linked with version 3.0.14.
│ This might cause Julia to terminate when working with
│ sparse matrix factorizations, e.g. solving systems of
│ equations with \.
│
│ It is recommended that you use Julia with the same major
│ version of CHOLMOD as the one used during the build, or
│ download the generic binaries from www.julialang.org,
│ which ship with the correct versions of all dependencies.
└ @ SparseArrays.CHOLMOD ~/mambaforge/envs/julia-test/share/julia/stdlib/v1.10/SparseArrays/src/solvers/cholmod.jl:206
```
When not forcing conda-forge (which I expect to have issues anyway) I get:
```
julia> using SparseArrays
ERROR: InitError: could not load library "@rpath/libspqr.2.dylib"
dlopen(@rpath/libspqr.2.dylib, 0x0001): Library not loaded: @rpath/libtbb.dylib
Referenced from: /Users/mharradon/mambaforge/envs/julia-test/lib/libspqr.2.0.9.dylib
Reason: tried: '/Users/mharradon/mambaforge/envs/julia-test/lib/libtbb.dylib' (no such file), '/Users/mharradon/mambaforge/envs/julia-test/lib/libtbb.dylib' (no such file), '/Users/mharradon/mambaforge/envs/julia-test/lib/julia/libtbb.dylib' (no such file), '/Users/mharradon/mambaforge/envs/julia-test/lib/libtbb.dylib' (no such file), '/System/Volumes/Preboot/Cryptexes/OS/Users/mharradon/mambaforge/envs/julia-test/lib/libtbb.dylib' (no such file), '/Users/mharradon/mambaforge/envs/julia-test/lib/julia/../libtbb.dylib' (no such file), '/Users/mharradon/mambaforge/envs/julia-test/lib/libtbb.dylib' (no such file), '/usr/local/lib/libtbb.dylib' (no such file), '/usr/lib/libtbb.dylib' (no such file, not in dyld cache)
Stacktrace:
[1] dlopen(s::String, flags::UInt32; throw_error::Bool)
@ Base.Libc.Libdl ./libdl.jl:117
[2] dlopen
@ ./libdl.jl:116 [inlined]
[3] dlopen(s::String)
@ Base.Libc.Libdl ./libdl.jl:116
[4] __init__()
@ SuiteSparse_jll ~/mambaforge/envs/julia-test/share/julia/stdlib/v1.10/SuiteSparse_jll/src/SuiteSparse_jll.jl:104
[5] run_module_init(mod::Module, i::Int64)
@ Base ./loading.jl:1134
[6] register_restored_modules(sv::Core.SimpleVector, pkg::Base.PkgId, path::String)
@ Base ./loading.jl:1122
[7] _include_from_serialized(pkg::Base.PkgId, path::String, ocachepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1067
[8] _tryrequire_from_serialized(modkey::Base.PkgId, path::String, ocachepath::String, sourcepath::String, depmods::Vector{Any})
@ Base ./loading.jl:1481
[9] _require_search_from_serialized(pkg::Base.PkgId, sourcepath::String, build_id::UInt128)
@ Base ./loading.jl:1574
[10] _require(pkg::Base.PkgId, env::String)
@ Base ./loading.jl:1938
[11] __require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1812
[12] #invoke_in_world#3
@ ./essentials.jl:926 [inlined]
[13] invoke_in_world
@ ./essentials.jl:923 [inlined]
[14] _require_prelocked(uuidkey::Base.PkgId, env::String)
@ Base ./loading.jl:1803
[15] macro expansion
@ ./loading.jl:1790 [inlined]
[16] macro expansion
@ ./lock.jl:267 [inlined]
[17] __require(into::Module, mod::Symbol)
@ Base ./loading.jl:1753
[18] #invoke_in_world#3
@ ./essentials.jl:926 [inlined]
[19] invoke_in_world
@ ./essentials.jl:923 [inlined]
[20] require(into::Module, mod::Symbol)
@ Base ./loading.jl:1746
during initialization of module SuiteSparse_jll
```
### Installed packages
```shell
arpack conda-forge/osx-64::arpack-3.8.0-nompi_hb44a6d1_101
bzip2 conda-forge/osx-64::bzip2-1.0.8-h10d778d_5
c-ares conda-forge/osx-64::c-ares-1.27.0-h10d778d_0
ca-certificates conda-forge/osx-64::ca-certificates-2024.2.2-h8857fd0_0
curl conda-forge/osx-64::curl-8.7.1-h726d00d_0
gettext conda-forge/osx-64::gettext-0.21.1-h8a4c099_0
git conda-forge/osx-64::git-2.44.0-pl5321h8687b19_0
gmp conda-forge/osx-64::gmp-6.3.0-h73e2aa4_1
icu conda-forge/osx-64::icu-73.2-hf5e326d_0
julia conda-forge/osx-64::julia-1.10.2-h7cbd117_1
krb5 conda-forge/osx-64::krb5-1.21.2-hb884880_0
libblas conda-forge/osx-64::libblas-3.9.0-21_osx64_openblas
libcblas conda-forge/osx-64::libcblas-3.9.0-21_osx64_openblas
libcurl conda-forge/osx-64::libcurl-8.7.1-h726d00d_0
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libedit conda-forge/osx-64::libedit-3.1.20191231-h0678c8f_2
libev conda-forge/osx-64::libev-4.33-h10d778d_2
libexpat conda-forge/osx-64::libexpat-2.6.2-h73e2aa4_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
libhwloc conda-forge/osx-64::libhwloc-2.9.3-default_h24e0189_1009
libiconv conda-forge/osx-64::libiconv-1.17-hd75f5a5_2
liblapack conda-forge/osx-64::liblapack-3.9.0-21_osx64_openblas
libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_1
libopenblas conda-forge/osx-64::libopenblas-0.3.26-openmp_hfef2a42_0
libopenblas-ilp64 conda-forge/osx-64::libopenblas-ilp64-0.3.26-openmp_h17068ef_0
libopenlibm4 conda-forge/osx-64::libopenlibm4-0.8.1-h10d778d_1
libosxunwind conda-forge/osx-64::libosxunwind-0.0.6-h940c156_0
libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0
libutf8proc conda-forge/osx-64::libutf8proc-2.8.0-hb7f2c08_0
libxml2 conda-forge/osx-64::libxml2-2.12.6-hc0ae0f7_1
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.2-hb6ac08f_0
metis conda-forge/osx-64::metis-5.1.0-he965462_1007
mpfr conda-forge/osx-64::mpfr-4.2.1-h0c69b56_0
ncurses conda-forge/osx-64::ncurses-6.4.20240210-h73e2aa4_0
openblas-ilp64 conda-forge/osx-64::openblas-ilp64-0.3.26-openmp_ha601604_0
openlibm conda-forge/osx-64::openlibm-0.8.1-h10d778d_1
openssl conda-forge/osx-64::openssl-3.2.1-hd75f5a5_1
p7zip conda-forge/osx-64::p7zip-16.02-he49afe7_1001
pcre2 conda-forge/osx-64::pcre2-10.43-h0ad2156_0
perl conda-forge/osx-64::perl-5.32.1-7_h10d778d_perl5
suitesparse conda-forge/osx-64::suitesparse-5.10.1-h4bf45ed_3
tbb conda-forge/osx-64::tbb-2021.11.0-h7728843_1
xz conda-forge/osx-64::xz-5.2.6-h775f41a_0
zlib conda-forge/osx-64::zlib-1.2.13-h8a1eda9_5
zstd conda-forge/osx-64::zstd-1.5.5-h829000d_0
Not forcing channel:
arpack conda-forge/osx-64::arpack-3.8.0-nompi_hb44a6d1_101
blas main/osx-64::blas-1.0-openblas
bzip2 main/osx-64::bzip2-1.0.8-h6c40b1e_5
c-ares conda-forge/osx-64::c-ares-1.27.0-h10d778d_0
ca-certificates main/osx-64::ca-certificates-2024.3.11-hecd8cb5_0
curl main/osx-64::curl-8.5.0-h04015c4_0
gdbm main/osx-64::gdbm-1.18-hdccc71a_4
gettext main/osx-64::gettext-0.21.0-he85b6c0_1
git conda-forge/osx-64::git-2.44.0-pl5321h8687b19_0
gmp conda-forge/osx-64::gmp-6.3.0-h73e2aa4_1
icu main/osx-64::icu-73.1-hcec6c5f_0
julia conda-forge/osx-64::julia-1.10.2-h7cbd117_1
krb5 main/osx-64::krb5-1.20.1-h428f121_1
libblas conda-forge/osx-64::libblas-3.9.0-21_osx64_openblas
libcurl main/osx-64::libcurl-8.5.0-hf20ceda_0
libcxx conda-forge/osx-64::libcxx-16.0.6-hd57cbcb_0
libedit main/osx-64::libedit-3.1.20230828-h6c40b1e_0
libev main/osx-64::libev-4.33-h9ed2024_1
libexpat conda-forge/osx-64::libexpat-2.6.2-h73e2aa4_0
libgfortran conda-forge/osx-64::libgfortran-5.0.0-13_2_0_h97931a8_3
libgfortran5 conda-forge/osx-64::libgfortran5-13.2.0-h2873a65_3
libiconv conda-forge/osx-64::libiconv-1.17-hd75f5a5_2
liblapack conda-forge/osx-64::liblapack-3.9.0-21_osx64_openblas
libnghttp2 conda-forge/osx-64::libnghttp2-1.58.0-h64cf6d3_1
libopenblas conda-forge/osx-64::libopenblas-0.3.26-openmp_hfef2a42_0
libopenblas-ilp64 conda-forge/osx-64::libopenblas-ilp64-0.3.26-openmp_h17068ef_0
libopenlibm4 conda-forge/osx-64::libopenlibm4-0.8.1-h10d778d_1
libosxunwind conda-forge/osx-64::libosxunwind-0.0.6-h940c156_0
libssh2 conda-forge/osx-64::libssh2-1.11.0-hd019ec5_0
libutf8proc conda-forge/osx-64::libutf8proc-2.8.0-hb7f2c08_0
libxml2 main/osx-64::libxml2-2.10.4-h1bd7e62_1
libzlib conda-forge/osx-64::libzlib-1.2.13-h8a1eda9_5
llvm-openmp conda-forge/osx-64::llvm-openmp-18.1.2-hb6ac08f_0
metis main/osx-64::metis-5.1.0-h0a44026_4
mpfr conda-forge/osx-64::mpfr-4.2.1-h0c69b56_0
ncurses main/osx-64::ncurses-6.4-hcec6c5f_0
openblas-ilp64 conda-forge/osx-64::openblas-ilp64-0.3.26-openmp_ha601604_0
openlibm conda-forge/osx-64::openlibm-0.8.1-h10d778d_1
openssl conda-forge/osx-64::openssl-3.2.1-hd75f5a5_1
p7zip main/osx-64::p7zip-16.02-hcec6c5f_0
pcre2 conda-forge/osx-64::pcre2-10.43-h0ad2156_0
perl main/osx-64::perl-5.34.0-h435f0c2_2
readline main/osx-64::readline-8.2-hca72f7f_0
suitesparse main/osx-64::suitesparse-5.10.1-h577c77e_2
tbb main/osx-64::tbb-2021.8.0-ha357a0b_0
xz main/osx-64::xz-5.4.6-h6c40b1e_0
zlib conda-forge/osx-64::zlib-1.2.13-h8a1eda9_5
```
### Environment info
```shell
active environment : julia-test
active env location : /Users/mharradon/mambaforge/envs/julia-test
shell level : 3
user config file : /Users/mharradon/.condarc
populated config files : /Users/mharradon/mambaforge/.condarc
/Users/mharradon/.condarc
conda version : 23.11.0
conda-build version : 3.28.2
python version : 3.10.10.final.0
solver : libmamba (default)
virtual packages : __archspec=1=skylake
__conda=23.11.0=0
__osx=14.4.1=0
__unix=0=0
base environment : /Users/mharradon/mambaforge (writable)
conda av data dir : /Users/mharradon/mambaforge/etc/conda
conda av metadata url : None
channel URLs : https://conda.anaconda.org/main/osx-64
https://conda.anaconda.org/main/noarch
https://conda.anaconda.org/conda-forge/osx-64
https://conda.anaconda.org/conda-forge/noarch
package cache : /Users/mharradon/mambaforge/pkgs
/Users/mharradon/.conda/pkgs
envs directories : /Users/mharradon/mambaforge/envs
/Users/mharradon/.conda/envs
platform : osx-64
user-agent : conda/23.11.0 requests/2.28.2 CPython/3.10.10 Darwin/23.4.0 OSX/14.4.1 solver/libmamba conda-libmamba-solver/23.12.0 libmambapy/1.5.6
UID:GID : 1647354838:187400128
netrc file : None
offline mode : False
```
Thanks for taking a look!
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